Update: I solved the problem now with the MPEG4 codec for those of my videos that had that issue. While doing so I ran into the problem that Youtube doesn't offer import/export of annotations, thus no way to copy over annotations from the badly encoded video to the cleaned up one, luckily there is a workaround. This video explains how one can import and export annotations. Short summary, usehttp://www.google.com/reviews/y/read2?video_id=YOUR_VIDEO_ID_HERE to get an xml of your annotation and then the Firefox Tamper Data Add-On to fudge your annotations into a POST request.

Update: Two questions on the YouTube help forum referencing this problem:

5 comments:

Same problem, at least with most of the containers and codecs I have tried. Using ffmpeg to create a flv container seems like it might work, but requires a reencode of the video (-vcodec copy produces something that Youtube doesn't understand).